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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ), 'gf_id' => 'HOM05D001312', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001312' ), 'data_identifier' => 'HOM05D001312', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001312', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '478', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p26830' => 'bna', 'A02p01520' => 'bna', 'A03p01370' => 'bna', 'A03p05600' => 'bna', 'A03p10880' => 'bna', 'A10p25420' => 'bna', 'A10p32330' => 'bna', 'Aa31LG1G21490' => 'aar', 'Aa31LG3G14830' => 'aar', 'Aa31LG4G14290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3661' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.3849' => 'aag', 'Actinidia00821' => 'ach', 'Actinidia03681' => 'ach', 'Actinidia03682' => 'ach', 'Actinidia06935' => 'ach', 'Actinidia06936' => 'ach', 'Actinidia07206' => 'ach', 'Actinidia16356' => 'ach', 'Actinidia24175' => 'ach', 'Actinidia39872' => 'ach', 'Ah.01g016710' => 'amhyb', 'Ah.06g194370' => 'amhyb', 'Ah.15g091190' => 'amhyb', 'AL5G23240' => 'aly', 'AL6G13310' => 'aly', 'AL6G23200' => 'aly', 'AL6G33760' => 'aly', 'Aqoxy1G00966' => 'aox', 'Aqoxy1G00967' => 'aox', 'Aqoxy2G00289' => 'aox', 'arahy.Tifrunner.gnm1.ann1.42C0B0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9KY8ZW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9N20R9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A1GHB6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BS1MHB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1UQYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IWGZ26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UY40LW' => 'arhy', 'AT5G03770' => 'ath', 'AT5G12400' => 'ath', 'AT5G22760' => 'ath', 'AT5G35210' => 'ath', 'ATR0721G002' => 'atr', 'ATR0820G030' => 'atr', 'ATR0820G168' => 'atr', 'Atru.BG.216.p' => 'acertr', 'Atru.chr3.2620' => 'acertr', 'Atru.chr3.3397' => 'acertr', 'Atru.chr3.3398' => 'acertr', 'Atru.chr3.3399' => 'acertr', 'Atru.chr3.3400' => 'acertr', 'Atru.chr8.1664' => 'acertr', 'AUR62000168' => 'cqu', 'AUR62023958' => 'cqu', 'AUR62031754' => 'cqu', 'AUR62033601' => 'cqu', 'AUR62037894' => 'cqu', 'AUR62039843' => 'cqu', 'BcaB01g04696' => 'bca', 'BcaB01g05404' => 'bca', 'BcaB05g22698' => 'bca', 'BcaB05g23039' => 'bca', 'BcaB05g23042' => 'bca', 'BcaB05g23648' => 'bca', 'BcaB08g37000' => 'bca', 'BcaC01g06570' => 'bca', 'BcaC03g13911' => 'bca', 'BcaC04g19184' => 'bca', 'BcaC06g32083' => 'bca', 'BcaC09g49653' => 'bca', 'BcaNung01192' => 'bca', 'BcaNung03614' => 'bca', 'BcaNung03615' => 'bca', 'BcaNung03616' => 'bca', 'BcaNung03617' => 'bca', 'BcaNung03620' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p00420' => 'bna', 'BolC1t03389H' => 'bol', 'BolC2t06519H' => 'bol', 'BolC2t07191H' => 'bol', 'BolC3t12726H' => 'bol', 'BolC3t13155H' => 'bol', 'BolC3t13720H' => 'bol', 'BolC9t59283H' => 'bol', 'BolC9t60051H' => 'bol', 'BraA01t02612Z' => 'bra', 'BraA02t05132Z' => 'bra', 'BraA02t05684Z' => 'bra', 'BraA03t09516Z' => 'bra', 'BraA03t09897Z' => 'bra', 'BraA03t10398Z' => 'bra', 'BraA10t44606Z' => 'bra', 'BraA10t45274Z' => 'bra', 'C01p34190' => 'bna', 'C02p05740' => 'bna', 'C02p11190' => 'bna', 'C02p11200' => 'bna', 'C02p11210' => 'bna', 'C02p11220' => 'bna', 'C03p01710' => 'bna', 'C03p06550' => 'bna', 'C03p12520' => 'bna', 'C09p64490' => 'bna', 'C09p73160' => 'bna', 'CAN.G175.8' => 'can', 'CAN.G47.9' => 'can', 'CAN.G633.5' => 'can', 'CAN.G644.40' => 'can', 'CAN.G839.1' => 'can', 'CAN.G919.4' => 'can', 'CANSAT64G1407' => 'cansat', 'CANSAT80G2114' => 'cansat', 'CARHR190830' => 'chi', 'CARHR200700' => 'chi', 'CARHR208850' => 'chi', 'CARHR208860' => 'chi', 'CARHR208870' => 'chi', 'CARHR209530' => 'chi', 'CARHR211510' => 'chi', 'Carub.0005s1053' => 'cru', 'Carub.0006s0268' => 'cru', 'Carub.0006s1090' => 'cru', 'Carub.0006s2047' => 'cru', 'Ca_01686_v3' => 'car', 'Ca_11247_v3' => 'car', 'Ca_11617_v3' => 'car', 'Ca_18983_v3' => 'car', 'Ca_19363_v3' => 'car', 'Ca_30478_v3' => 'car', 'CBR_g33928' => 'cbr', 'CBR_g874' => 'cbr', 'Cc01_g05990' => 'ccan', 'Cc01_g09930' => 'ccan', 'Cc06_g05050' => 'ccan', 'CDE02G0321' => 'cde', 'CDE02G1913' => 'cde', 'CDE02G1918' => 'cde', 'CDE02G2461' => 'cde', 'CDE02G3010' => 'cde', 'CDE06G0794' => 'cde', 'CDE08G0703' => 'cde', 'Cfa009825' => 'cfa', 'Cfa010099' => 'cfa', 'Ciclev10013092m.g' => 'ccl', 'Ciclev10014020m.g' => 'ccl', 'Ciclev10027677m.g' => 'ccl', 'Ciclev10032390m.g' => 'ccl', 'CiPaw.09G007400' => 'cil', 'CiPaw.10G004200' => 'cil', 'CiPaw.13G141900' => 'cil', 'CiPaw.13G153400' => 'cil', 'CiPaw.14G104300' => 'cil', 'CiPaw.14G115800' => 'cil', 'ClCG02G021830' => 'cla', 'ClCG03G012960' => 'cla', 'ClCG04G009690' => 'cla', 'COL.COLO4_19275' => 'col', 'COL.COLO4_22294' => 'col', 'COL.COLO4_36486' => 'col', 'Cpa.g.c36658' => 'cpa', 'Cpa.g.sc47.58' => 'cpa', 'Cpa.g.sc5.99' => 'cpa', 'Cpa.g.sc84.8' => 'cpa', 'Cre05.g247000' => 'cre', 'Cre13.g583100' => 'cre', 'CsaV3_1G043090' => 'csa', 'CsaV3_6G014620' => 'csa', 'CsaV3_6G040350' => 'csa', 'CSS0005615' => 'camsi', 'CSS0009438' => 'camsi', 'CSS0018354' => 'camsi', 'CSS0027895' => 'camsi', 'CSS0032749' => 'camsi', 'CSS0034096' => 'camsi', 'CSS0034120' => 'camsi', 'DCAR_000407' => 'dca', 'DCAR_006144' => 'dca', 'DCAR_015029' => 'dca', 'DCAR_015030' => 'dca', 'DCAR_018746' => 'dca', 'DCAR_022735' => 'dca', 'DCAR_023770' => 'dca', 'Dinv06117' => 'din', 'Dinv12438' => 'din', 'Dinv12534' => 'din', 'Dinv12537' => 'din', 'Dinv19769' => 'din', 'Dinv22150' => 'din', 'Dinv29412' => 'din', 'Dinv29413' => 'din', 'Dinv35859' => 'din', 'Dinv36206' => 'din', 'Duzib168G2332' => 'dzi', 'ECA233G2461' => 'eca', 'ECA248G0607' => 'eca', 'ECA248G1880' => 'eca', 'ECA248G2284' => 'eca', 'EL10Ac4g10179' => 'bvu', 'EL10Ac7g16768' => 'bvu', 'EL10Ac9g21057' => 'bvu', 'Eucgr.A01566' => 'egr', 'Eucgr.J00416' => 'egr', 'Eucgr.J00728' => 'egr', 'FAN02G1263' => 'fan', 'FAN05G0775' => 'fan', 'FAN05G3053' => 'fan', 'FAN09G2766' => 'fan', 'FAN11G1475' => 'fan', 'FAN11G4030' => 'fan', 'FAN14G3191' => 'fan', 'FAN16G2071' => 'fan', 'FAN16G2548' => 'fan', 'FAN21G0684' => 'fan', 'FAN21G2146' => 'fan', 'FAN25G0002' => 'fan', 'FAN25G1359' => 'fan', 'FvH4_3g28290' => 'fve', 'FvH4_3g30100' => 'fve', 'FvH4_6g17520' => 'fve', 'Glyma.10G065300' => 'gma', 'Glyma.11G095800' => 'gma', 'Glyma.11G190000' => 'gma', 'Glyma.12G021900' => 'gma', 'Glyma.12G084300' => 'gma', 'Glyma.12G180700' => 'gma', 'Glyma.13G150200' => 'gma', 'Glyma.13G320100' => 'gma', 'Gohir.A04G066728' => 'ghi', 'Gohir.A07G122300' => 'ghi', 'Gohir.A07G122400' => 'ghi', 'Gohir.A07G122450' => 'ghi', 'Gohir.A07G122500' => 'ghi', 'Gohir.A09G092100' => 'ghi', 'Gohir.D04G105500' => 'ghi', 'Gohir.D07G126400' => 'ghi', 'Gohir.D07G126500' => 'ghi', 'Gohir.D09G091966' => 'ghi', 'Gohir.D09G092032' => 'ghi', 'Gorai.001G136300' => 'gra', 'Gorai.001G136400' => 'gra', 'Gorai.006G108600' => 'gra', 'Gorai.009G409200' => 'gra', 'GSVIVG01031411001' => 'vvi', 'GSVIVG01033751001' => 'vvi', 'GSVIVG01037231001' => 'vvi', 'HanXRQChr01g0016711' => 'han', 'HanXRQChr01g0016741' => 'han', 'HanXRQChr01g0028401' => 'han', 'HanXRQChr10g0319711' => 'han', 'HanXRQChr11g0346711' => 'han', 'HanXRQChr12g0378141' => 'han', 'Haze_19515' => 'cav', 'Haze_23185' => 'cav', 'Haze_23465' => 'cav', 'Hma1.2p1_0181F.1_g079960' => 'hma', 'Hma1.2p1_0651F.1_g195720' => 'hma', 'Hma1.2p1_1920F.1_g307520' => 'hma', 'Hma1.2p1_1920F.1_g307530' => 'hma', 'Hma1.2p1_1920F.1_g307540' => 'hma', 'Hma1.2p1_2309F.1_g319530' => 'hma', 'HPP92_006792' => 'vpl', 'HPP92_006796' => 'vpl', 'HPP92_012111' => 'vpl', 'HPP92_017974' => 'vpl', 'HPP92_026720' => 'vpl', 'HPP92_026721' => 'vpl', 'Hund07715' => 'sun', 'Hund20444' => 'sun', 'Hund21993' => 'sun', 'Lalb_Chr01g0004711' => 'lal', 'Lalb_Chr03g0024551' => 'lal', 'Lalb_Chr03g0027881' => 'lal', 'Lalb_Chr19g0139691' => 'lal', 'Lalb_Chr21g0315421' => 'lal', 'Lalb_Chr21g0315431' => 'lal', 'Lalb_Chr21g0315441' => 'lal', 'Lj1A305G17' => 'lonja', 'Lj1C219T5' => 'lonja', 'Lj3A1005G38' => 'lonja', 'Lj3g0003552' => 'lja', 'Lj3g0017534' => 'lja', 'Lj5g0006635' => 'lja', 'Lsat_1_v5_gn_1_50640' => 'lsa', 'Lsat_1_v5_gn_1_61921' => 'lsa', 'Lsat_1_v5_gn_2_51501' => 'lsa', 'Lsat_1_v5_gn_6_71181' => 'lsa', 'Manes.04G010300' => 'mes', 'Manes.06G161100' => 'mes', 'Manes.08G018900' => 'mes', 'Manes.11G155800' => 'mes', 'Manes.14G005800' => 'mes', 'Mapoly0002s0209' => 'mpo', 'Mapoly0044s0125' => 'mpo', 'MBI01_g23067_MAGBIO' => 'mbi', 'MBI01_g48091_MAGBIO' => 'mbi', 'MD03G1132800' => 'mdo', 'MD03G1169900' => 'mdo', 'MD11G1155100' => 'mdo', 'MD11G1187100' => 'mdo', 'MD14G1093900' => 'mdo', 'Medtr1g061560' => 'mtr', 'Medtr2g084615' => 'mtr', 'Medtr2g084620' => 'mtr', 'Medtr2g084660' => 'mtr', 'Medtr4g055900' => 'mtr', 'Medtr4g055910' => 'mtr', 'Medtr4g055920' => 'mtr', 'Medtr4g076180' => 'mtr', 'MELO3C015157.2' => 'cme', 'MELO3C021462.2' => 'cme', 'MELO3C024510.2' => 'cme', 'Migut.D00642' => 'egut', 'Migut.D02327' => 'egut', 'Migut.J00495' => 'egut', 'Migut.N02359' => 'egut', 'Migut.N02361' => 'egut', 'Migut.N02523' => 'egut', 'MSTRG.17625' => 'ama', 'MSTRG.21070' => 'ama', 'MSTRG.21072' => 'ama', 'MSTRG.21358' => 'ama', 'MSTRG.5801' => 'ama', 'Nitab4.5_0000132g0320' => 'nta', 'Nitab4.5_0000442g0240' => 'nta', 'Nitab4.5_0002571g0030' => 'nta', 'Nitab4.5_0002726g0060' => 'nta', 'Nitab4.5_0003470g0010' => 'nta', 'Nitab4.5_0004490g0050' => 'nta', 'Nitab4.5_0004926g0010' => 'nta', 'Nitab4.5_0006878g0030' => 'nta', 'Nn2g13967' => 'nnu', 'Nn6g35082' => 'nnu', 'Nn6g35083' => 'nnu', 'Nn7g36465' => 'nnu', 'Nn7g37428' => 'nnu', 'Oeu001484.2' => 'oeu', 'Oeu016685.1' => 'oeu', 'Oeu016686.1' => 'oeu', 'Oeu035532.1' => 'oeu', 'Oeu038110.1' => 'oeu', 'Oeu039841.2' => 'oeu', 'Os01g0857300' => 'osa', 'Os07g0661550' => 'osa', 'Os11g0148700' => 'osa', 'Os11g0148800' => 'osa', 'Peaxi162Scf00004g03915' => 'pax', 'Peaxi162Scf00004g03919' => 'pax', 'Peaxi162Scf00004g03921' => 'pax', 'Peaxi162Scf00110g01214' => 'pax', 'Peaxi162Scf00157g00417' => 'pax', 'Peaxi162Scf00789g00216' => 'pax', 'PGR119G0461' => 'pgr', 'PGR119G2014' => 'pgr', 'PGSC0003DMG400007126' => 'stu', 'PGSC0003DMG400028176' => 'stu', 'Phvul.005G128100' => 'pvu', 'Phvul.007G224100' => 'pvu', 'Phvul.011G023900' => 'pvu', 'Phvul.011G089300' => 'pvu', 'Potri.001G254300' => 'ptr', 'Potri.004G189600' => 'ptr', 'Potri.009G049100' => 'ptr', 'Potri.009G150200' => 'ptr', 'Potri.016G095900' => 'ptr', 'Pp3c21_8090' => 'ppa', 'Pp3c7_5480' => 'ppa', 'PRCOL_00000281' => 'pco', 'Prupe.4G257200' => 'ppe', 'Prupe.6G117600' => 'ppe', 'Prupe.7G120300' => 'ppe', 'Psat5g255240' => 'psa', 'Psat6g076240' => 'psa', 'Psat6g218640' => 'psa', 'Psat7g143680' => 'psa', 'Psat7g179760' => 'psa', 'PSO063G1518' => 'pso', 'PSO063G2793' => 'pso', 'PSO339G1313' => 'pso', 'PSO339G2353' => 'pso', 'PSO339G3022' => 'pso', 'PSO384G1094' => 'pso', 'QL01p014004' => 'qlo', 'QL01p018031' => 'qlo', 'QL07p040881' => 'qlo', 'RcHm_v2.0_Chr3g0471781' => 'rch', 'RcHm_v2.0_Chr5g0051171' => 'rch', 'RcHm_v2.0_Chr5g0055621' => 'rch', 'Rhsim01G0209200' => 'rsi', 'Rhsim03G0083100' => 'rsi', 'Rhsim13G0104700' => 'rsi', 'Rhsim13G0217000' => 'rsi', 'Sabra04G0128400' => 'sbr', 'Sabra09G0035800' => 'sbr', 'Sabra09G0118900' => 'sbr', 'Sabra16G0101200' => 'sbr', 'Sabra16G0155000' => 'sbr', 'SalBow3G2703' => 'sbo', 'SalBow7G3318' => 'sbo', 'Sc02g0001220' => 'sci', 'Sc12g0003890' => 'sci', 'Sc16g0011180' => 'sci', 'Sc21g0004650' => 'sci', 'Sc21g0004660' => 'sci', 'Sed0012062' => 'sed', 'Sed0012905' => 'sed', 'Sed0017063' => 'sed', 'Sed0027883' => 'sed', 'SEGI_08770' => 'sgi', 'SEGI_09767' => 'sgi', 'SEGI_18852' => 'sgi', 'SEGI_32755' => 'sgi', 'SEGI_36901' => 'sgi', 'SGA_v2.0_scaffold27G11600' => 'sas', 'SGA_v2.0_scaffold29G12279' => 'sas', 'SGA_v2.0_scaffold40G15429' => 'sas', 'SGA_v2.0_scaffold8G04558' => 'sas', 'SHI06140' => 'shi', 'SMO115G0301' => 'smo', 'SMO352G0061' => 'smo', 'SMO364G0357' => 'smo', 'Solyc06g074640.2' => 'sly', 'Solyc10g083710.2' => 'sly', 'Solyc11g065160.3' => 'sly', 'Solyc11g066780.3' => 'sly', 'Sopen06g031060' => 'spe', 'Sopen10g033180' => 'spe', 'Sopen11g024880' => 'spe', 'Sopen11g024890' => 'spe', 'Sopen11g026500' => 'spe', 'Sp5g16400' => 'spa', 'Sp6g22660' => 'spa', 'Sp6g31240' => 'spa', 'Sp6g38960' => 'spa', 'TAR623G0291' => 'tar', 'TAR623G0760' => 'tar', 'TAR623G1731' => 'tar', 'TAR633G1314' => 'tar', 'THA.LOC104799531' => 'tha', 'THA.LOC104811188' => 'tha', 'THA.LOC104816378' => 'tha', 'Thecc.05G079000' => 'tca', 'Thecc.09G241500' => 'tca', 'Thecc.09G293200' => 'tca', 'Thhalv10012427m.g' => 'esa', 'Thhalv10012428m.g' => 'esa', 'Thhalv10013569m.g' => 'esa', 'TPR.G20748' => 'tpr', 'TPR.G20749' => 'tpr', 'TPR.G22567' => 'tpr', 'TPR.G32362' => 'tpr', 'TPR.G5684' => 'tpr', 'TWI23G1095' => 'twi', 'TWI39G0267' => 'twi', 'TWI53G1380' => 'twi', 'TWI75G0682' => 'twi', 'TWI79G1536' => 'twi', 'unitig_46.g18236' => 'ugi', 'unitig_744.g24689' => 'ugi', 'vmacro03225' => 'vma', 'vmacro04116' => 'vma', 'vmacro07336' => 'vma', 'vmacro14380' => 'vma', 'vmacro23022' => 'vma', 'vmacro23111' => 'vma', 'VMungo0251G1834' => 'vmu', 'VMungo0647G1894' => 'vmu', 'VMungo0720G0477' => 'vmu', 'VMungo1080G0366' => 'vmu', 'VMungo1127G0568' => 'vmu', 'VMungo1127G0765' => 'vmu', 'VMungo1127G2034' => 'vmu', 'Zm00001eb009840' => 'zma', 'Zm00001eb092810' => 'zma', 'Zm00001eb147410' => 'zma', 'Zm00001eb214600' => 'zma', 'Zm00001eb329910' => 'zma', 'Zm00001eb406520' => 'zma' ) $gf_id = 'HOM05D001312' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001312' ) $data_identifier = 'HOM05D001312' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 8, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 7, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 7, 'din' => (int) 10, 'dzi' => (int) 1, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 11, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 8, 'cme' => (int) 3, 'egut' => (int) 6, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406520' $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